Remove outdated deprecated resources (#3114)

All resources that have been deprecated before the release of `v1.0.0b1` have been removed. The remaining deprecations are updated to ensure they use the custom `AiidaDeprecationWarning` to prevent them from being filtered by default, as well as that the docstring reflects when the deprecation resources will be removed.
aiidateam · Jul 2, 2019 · 406dbb4 · 406dbb4
1 parent 4738116
commit 406dbb4
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Showing 23 changed files with 86 additions and 834 deletions.
diff --git a/aiida/__init__.py b/aiida/__init__.py
@@ -65,7 +65,7 @@ def load_dbenv(profile=None):
     :type profile: str
 
     .. deprecated:: 1.0.0
-        Will be removed in `v1.1.0`, use :func:`aiida.manage.configuration.load_profile` instead.
+        Will be removed in `v2.0.0`, use :func:`aiida.manage.configuration.load_profile` instead.
     """
     warnings.warn('function is deprecated, use `load_profile` instead', AiidaDeprecationWarning)  # pylint: disable=no-member
     current_profile = get_profile()
@@ -88,7 +88,7 @@ def try_load_dbenv(profile=None):
 
 
     .. deprecated:: 1.0.0
-        Will be removed in `v1.1.0`, use :func:`aiida.manage.configuration.load_profile` instead.
+        Will be removed in `v2.0.0`, use :func:`aiida.manage.configuration.load_profile` instead.
     """
     warnings.warn('function is deprecated, use `load_profile` instead', AiidaDeprecationWarning)  # pylint: disable=no-member
     if not is_dbenv_loaded():
@@ -103,7 +103,7 @@ def is_dbenv_loaded():
     :rtype: bool
 
     .. deprecated:: 1.0.0
-        Will be removed in `v1.1.0`, use :func:`aiida.manage.configuration.load_profile` instead.
+        Will be removed in `v2.0.0`, use :func:`aiida.manage.configuration.load_profile` instead.
     """
     warnings.warn('function is deprecated, use `load_profile` instead', AiidaDeprecationWarning)  # pylint: disable=no-member
     return get_profile() is not None

diff --git a/aiida/backends/general/abstractqueries.py b/aiida/backends/general/abstractqueries.py
@@ -166,8 +166,7 @@ def get_bands_and_parents_structure(self, args):
         if args.group_pk is not None:
             group_filters.update({"id": {"in": args.group_pk}})
         if group_filters:
-            qb.append(orm.Group, tag="group", filters=group_filters,
-                      group_of="bdata")
+            qb.append(orm.Group, tag="group", filters=group_filters, with_node="bdata")
 
         qb.append(orm.StructureData, tag="sdata", with_descendants="bdata",
                   # We don't care about the creator of StructureData

diff --git a/aiida/backends/profile.py b/aiida/backends/profile.py
@@ -18,7 +18,9 @@
 
 import warnings
 
-warnings.warn('this module is deprecated', DeprecationWarning)  # pylint: disable=no-member
+from aiida.common.warnings import AiidaDeprecationWarning
+
+warnings.warn('this module is deprecated', AiidaDeprecationWarning)  # pylint: disable=no-member
 
 # Possible choices for backend
 BACKEND_DJANGO = 'django'
@@ -31,4 +33,4 @@
 # the attributes here fixes the problem, even though we have absolutely no idea why. Given that the module is deprecated
 # anyway and will soon be removed at which point the problem should no longer exist.
 run = None
-runctx = None
+runctx = None
diff --git a/aiida/backends/sqlalchemy/tests/test_generic.py b/aiida/backends/sqlalchemy/tests/test_generic.py
@@ -181,6 +181,6 @@ def test_group_batch_size(self):
         # correct addition.
         batch_sizes = (1, 3, 10, 1000)
         for batch_size in batch_sizes:
-            group = Group(name='test_batches_' + str(batch_size)).store()
+            group = Group(label='test_batches_' + str(batch_size)).store()
             group.backend_entity.add_nodes(nodes, skip_orm=True, batch_size=batch_size)
             self.assertEqual(set(_.pk for _ in nodes), set(_.pk for _ in group.nodes))
diff --git a/aiida/backends/tests/cmdline/commands/test_data.py b/aiida/backends/tests/cmdline/commands/test_data.py
@@ -285,7 +285,7 @@ def test_arrayshow(self):
 
 class TestVerdiDataBands(AiidaTestCase, TestVerdiDataListable):
     """
-    Testing verdi data bands 
+    Testing verdi data bands
     """
 
     @staticmethod
@@ -324,7 +324,7 @@ def connect_structure_bands(structure):
 
             k = KpointsData()
             k.set_cell(cell)
-            k.set_kpoints_path([('G', 'M', 2)])
+            k.set_kpoints([[0.,0.,0.],[0.1,0.1,0.1]])
 
             b = BandsData()
             b.set_kpointsdata(k)
@@ -412,7 +412,7 @@ def test_dictshow(self):
 
 class TestVerdiDataRemote(AiidaTestCase):
     """
-    Testing verdi data remote 
+    Testing verdi data remote
     """
 
     @classmethod

diff --git a/aiida/backends/tests/test_dataclasses.py b/aiida/backends/tests/test_dataclasses.py
@@ -3111,52 +3111,6 @@ class TestKpointsData(AiidaTestCase):
     Tests the KpointsData objects.
     """
 
-    def test_set_kpoints_path_legacy(self):
-        """
-        Regression test for the deprecated KpointsData.set_kpoints_path method.
-        For certain formats of a direct kpoint list, it is not necessary to have defined a cell.
-        """
-        import numpy
-        from aiida.orm.nodes.data.array.kpoints import KpointsData
-
-        # Create a node with two arrays
-        kpoints_01 = KpointsData()
-        kpoints_02 = KpointsData()
-        kpoints_03 = KpointsData()
-        kpoints_04 = KpointsData()
-
-        # The various allowed formats
-        format_01 = [('G', 'M')]
-        format_02 = [('G', 'M', 30)]
-        format_03 = [('G', (0, 0, 0), 'M', (1, 1, 1))]
-        format_04 = [('G', (0, 0, 0), 'M', (1, 1, 1), 30)]
-
-        # Without a cell defined, the first two should fail, the last two should work
-        with self.assertRaises(ValueError):
-            kpoints_01.set_kpoints_path(format_01)
-
-        with self.assertRaises(ValueError):
-            kpoints_02.set_kpoints_path(format_02)
-
-        kpoints_03.set_kpoints_path(format_03)
-        kpoints_04.set_kpoints_path(format_04)
-
-        # Define a cell and settings it enable the usage of formats 1 and 2
-        alat = 4.
-        cell = numpy.array([
-            [alat, 0., 0.],
-            [0., alat, 0.],
-            [0., 0., alat],
-        ])
-
-        kpoints_01.set_cell(cell)
-        kpoints_02.set_cell(cell)
-
-        kpoints_01.set_kpoints_path(format_01)
-        kpoints_02.set_kpoints_path(format_02)
-        kpoints_03.set_kpoints_path(format_03)
-        kpoints_04.set_kpoints_path(format_04)
-
     def test_mesh(self):
         """
         Check the methods to set and retrieve a mesh.
@@ -3279,63 +3233,6 @@ def test_kpoints_to_cartesian(self):
         klist = k.get_kpoints(cartesian=True)
         self.assertTrue(numpy.allclose(klist, input_klist, atol=1e-16))
 
-    def test_path(self):
-        """
-        Test the methods to generate automatically a list of kpoints
-        """
-        import numpy
-
-        k = KpointsData()
-
-        # shouldn't get anything wiothout having set the cell
-        with self.assertRaises(ValueError):
-            k.set_kpoints_path()
-
-        # define a cell
-        alat = 4.
-        cell = numpy.array([
-            [alat, 0., 0.],
-            [0., alat, 0.],
-            [0., 0., alat],
-        ])
-
-        k.set_cell(cell)
-        k.set_kpoints_path()
-        # something should be retrieved
-        klist = k.get_kpoints()
-
-        # test the various formats for specifying the path
-        k.set_kpoints_path([
-            ('G', 'M'),
-        ])
-        k.set_kpoints_path([
-            ('G', 'M', 30),
-        ])
-        k.set_kpoints_path([
-            ('G', (0., 0., 0.), 'M', (1., 1., 1.)),
-        ])
-        k.set_kpoints_path([
-            ('G', (0., 0., 0.), 'M', (1., 1., 1.), 30),
-        ])
-
-        # at least 2 points per segment
-        with self.assertRaises(ValueError):
-            k.set_kpoints_path([
-                ('G', 'M', 1),
-            ])
-        with self.assertRaises(ValueError):
-            k.set_kpoints_path([
-                ('G', (0., 0., 0.), 'M', (1., 1., 1.), 1),
-            ])
-
-        # try to set points with a spacing
-        k.set_kpoints_path(kpoint_distance=0.1)
-
-        # try to modify after storage
-        k.store()
-        with self.assertRaises(ModificationNotAllowed):
-            k.set_kpoints_path()
-
     def test_path_wrapper_legacy(self):
         """
         This is a clone of the test_path test but instead it goes through the new wrapper
@@ -3393,38 +3290,6 @@ def test_path_wrapper_legacy(self):
         # try to set points with a spacing
         get_explicit_kpoints_path(structure, method='legacy', kpoint_distance=0.1)
 
-    def test_tetra_x(self):
-        """
-        testing tetragonal cells with axis along X
-        """
-        import numpy
-        from aiida.plugins import DataFactory
-        alat = 1.5
-        cell_x = [[alat, 0, 0], [0, 1, 0], [0, 0, 1]]
-        K = DataFactory('array.kpoints')
-        k = K()
-        k.set_cell(cell_x)
-        points = k.get_special_points(cartesian=True)
-
-        self.assertAlmostEqual(points[0]['Z'][0], numpy.pi / alat)
-        self.assertAlmostEqual(points[0]['Z'][1], 0.)
-
-    def test_tetra_z(self):
-        """
-        testing tetragonal cells with axis along X
-        """
-        import numpy
-        from aiida.plugins import DataFactory
-        alat = 1.5
-        cell_x = [[1, 0, 0], [0, 1, 0], [0, 0, alat]]
-        K = DataFactory('array.kpoints')
-        k = K()
-        k.set_cell(cell_x)
-        points = k.get_special_points(cartesian=True)
-
-        self.assertAlmostEqual(points[0]['Z'][2], numpy.pi / alat)
-        self.assertAlmostEqual(points[0]['Z'][0], 0.)
-
     def test_tetra_z_wrapper_legacy(self):
         """
         This is a clone of the test_tetra_z test but instead it goes through the new wrapper
@@ -3757,7 +3622,7 @@ def test_band(self):
 
         k = KpointsData()
         k.set_cell(cell)
-        k.set_kpoints_path()
+        k.set_kpoints([[0.,0.,0.],[0.1,0.1,0.1]])
 
         b = BandsData()
         b.set_kpointsdata(k)
@@ -3800,7 +3665,7 @@ def test_export_to_file(self):
 
         k = KpointsData()
         k.set_cell(cell)
-        k.set_kpoints_path()
+        k.set_kpoints([[0.,0.,0.],[0.1,0.1,0.1]])
 
         b = BandsData()
         b.set_kpointsdata(k)

diff --git a/aiida/cmdline/commands/cmd_code.py b/aiida/cmdline/commands/cmd_code.py
@@ -11,6 +11,7 @@
 from __future__ import division
 from __future__ import print_function
 from __future__ import absolute_import
+
 from functools import partial
 import click
 import tabulate
@@ -19,7 +20,7 @@
 from aiida.cmdline.params import options, arguments
 from aiida.cmdline.params.options.commands import code as options_code
 from aiida.cmdline.utils import echo
-from aiida.cmdline.utils.decorators import with_dbenv, deprecated_command
+from aiida.cmdline.utils.decorators import with_dbenv
 from aiida.cmdline.utils.multi_line_input import ensure_scripts
 from aiida.common.exceptions import InputValidationError
 
@@ -208,15 +209,6 @@ def reveal(codes):
         echo.echo_success('Code<{}> {} revealed'.format(code.pk, code.full_label))
 
 
-@verdi_code.command()
-@arguments.CODE()
-@with_dbenv()
-@deprecated_command("Updating codes breaks data provenance. Use 'duplicate' instead.")
-# pylint: disable=unused-argument
-def update(code):
-    """Update an existing code."""
-
-
 @verdi_code.command()
 @arguments.CODE()
 @arguments.LABEL()
@@ -233,17 +225,6 @@ def relabel(code, label):
         echo.echo_success('Code<{}> relabeled from {} to {}'.format(code.pk, old_label, code.full_label))
 
 
-@verdi_code.command()
-@arguments.CODE()
-@arguments.LABEL()
-@with_dbenv()
-@click.pass_context
-@deprecated_command("This command may be removed in a future release. Use 'relabel' instead.")
-def rename(ctx, code, label):
-    """Rename a code."""
-    ctx.invoke(relabel, code=code, label=label)
-
-
 @verdi_code.command('list')
 @options.COMPUTER(help='Filter codes by computer.')
 @options.INPUT_PLUGIN(help='Filter codes by calculation input plugin.')

diff --git a/aiida/cmdline/commands/cmd_data/__init__.py b/aiida/cmdline/commands/cmd_data/__init__.py
@@ -11,24 +11,11 @@
 from __future__ import division
 from __future__ import print_function
 from __future__ import absolute_import
-import click
 
 from aiida.cmdline.commands.cmd_verdi import verdi
-from aiida.cmdline.commands.cmd_plugin import verdi_plugin
-from aiida.cmdline.utils import decorators
 from aiida.cmdline.utils.pluginable import Pluginable
 
 
 @verdi.group('data', entry_point_group='aiida.cmdline.data', cls=Pluginable)
 def verdi_data():
     """Inspect, create and manage data nodes."""
-
-
-@verdi_data.command('plugins')
-@click.argument('entry_point', type=click.STRING, required=False)
-@click.pass_context
-@decorators.with_dbenv()
-@decorators.deprecated_command("This command is deprecated. Use 'verdi plugin list' instead.")
-def data_plugins(ctx, entry_point):
-    """Print a list of registered data plugins or details of a specific data plugin."""
-    ctx.invoke(verdi_plugin.get_command(ctx, 'list'), entry_point_group='aiida.data', entry_point=entry_point)
diff --git a/aiida/engine/daemon/execmanager.py b/aiida/engine/daemon/execmanager.py
@@ -25,7 +25,6 @@
 from aiida.common.datastructures import CalcJobState
 from aiida.common.folders import SandboxFolder
 from aiida.common.links import LinkType
-from aiida.common.warnings import AiidaDeprecationWarning
 from aiida.orm import FolderData
 from aiida.orm.utils.log import get_dblogger_extra
 from aiida.plugins import DataFactory
@@ -252,9 +251,6 @@ def retrieve_calculation(calculation, transport, retrieved_temporary_folder):
     :param transport: an already opened transport to use for the retrieval.
     :param retrieved_temporary_folder: the absolute path to a directory in which to store the files
         listed, if any, in the `retrieved_temporary_folder` of the jobs CalcInfo
-
-    .. deprecated:: 1.0.0
-        `retrieve_singlefile_list` will be removed in `v2.0.0`, use `retrieve_temporary_list` instead.
     """
     logger_extra = get_dblogger_extra(calculation)
 
@@ -284,8 +280,6 @@ def retrieve_calculation(calculation, transport, retrieved_temporary_folder):
 
         # Second, retrieve the singlefiles, if any files were specified in the 'retrieve_temporary_list' key
         if retrieve_singlefile_list:
-            warnings.warn('`retrieve_singlefile_list` has been deprecated, use `retrieve_temporary_list` instead',
-                AiidaDeprecationWarning)  # pylint: disable=no-member
             with SandboxFolder() as folder:
                 _retrieve_singlefiles(calculation, transport, folder, retrieve_singlefile_list, logger_extra)